A method and apparatus for handling in-device co-existence interference in a user equipment are provided. In an exemplary method, a Long Term Evolution (LTE) activity scheduled to be performed during an inactive time period of an LTE module in a user equipment is determined. It is determined whether the LTE module is to be allowed to perform the LTE activity during the inactive time period. If the LTE activity is to be allowed, then the LTE module is allowed to perform the LTE activity during the inactive time period. Otherwise, the LTE module is not allowed to perform the LTE activity during the inactive time period to provide interference free time for an Industrial, Scientific and Medical (ISM) module in the user equipment. Moreover, the disallowed LTE activity is scheduled to be performed during an active time period following the inactive time period.